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Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. J Proteome Res 2023; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
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Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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3
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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Parkinson E, Aleksic M, Arthur R, Regufe Da Mota S, Cubberley R, Skipp PJ. Proteomic analysis of haptenation by skin sensitisers: Diphencyprone and ethyl acrylate. Toxicol In Vitro 2020; 62:104697. [DOI: 10.1016/j.tiv.2019.104697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023]
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5
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Yang EJ, Hendricks AJ, Beck KM, Shi VY. Bioactive: A new era of bioactive ingredients in topical formulations for inflammatory dermatoses. Dermatol Ther 2019; 32:e13101. [DOI: 10.1111/dth.13101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Eric J. Yang
- Department of DermatologyUniversity of California San Francisco San Francisco California
- Chicago Medical School, Rosalind Franklin University of Medicine and Science North Chicago Illinois
| | | | - Kristen M. Beck
- Department of DermatologyUniversity of California San Francisco San Francisco California
| | - Vivian Y. Shi
- Department of Medicine, Division of DermatologyUniversity of Arizona Tucson Arizona
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6
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Newton VL, Riba-Garcia I, Griffiths CEM, Rawlings AV, Voegeli R, Unwin RD, Sherratt MJ, Watson REB. Mass spectrometry-based proteomics reveals the distinct nature of the skin proteomes of photoaged compared to intrinsically aged skin. Int J Cosmet Sci 2019; 41:118-131. [PMID: 30661253 DOI: 10.1111/ics.12513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/15/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE With increasing age, skin is subject to alterations in its organization, which impact on its function as well as having clinical consequences. Proteomics is a useful tool for non-targeted, semi-quantitative simultaneous investigation of high numbers of proteins. In the current study, we utilize proteomics to characterize and contrast age-associated differences in photoexposed and photoprotected skin, with a focus on the epidermis, dermal-epidermal junction and papillary dermis. METHODS Skin biopsies from buttock (photoprotected) and forearm (photoexposed) of healthy volunteers (aged 18-30 or ≥65 years) were transversely sectioned from the stratum corneum to a depth of 250 μm. Following SDS-PAGE, each sample lane was segmented prior to analysis by liquid chromatography-mass spectrometry/mass spectrometry. Pathway analysis was carried out using Ingenuity IPA. RESULTS Comparison of skin proteomes at buttock and forearm sites revealed differences in relative protein abundance. Ageing in skin on the photoexposed forearm resulted in 80% of the altered proteins being increased with age, in contrast to the photoprotected buttock where 74% of altered proteins with age were reduced. Functionally, age-altered proteins in the photoexposed forearm were associated with conferring structure, energy and metabolism. In the photoprotected buttock, proteins associated with gene expression, free-radical scavenging, protein synthesis and protein degradation were most frequently altered. CONCLUSION This study highlights the necessity of not considering photoageing as an accelerated intrinsic ageing, but as a distinct physiological process.
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Affiliation(s)
- V L Newton
- Centre for Dermatology Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, and Salford Royal NHS Foundation Trust, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - I Riba-Garcia
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Core Technology facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT, UK
| | - C E M Griffiths
- Centre for Dermatology Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, and Salford Royal NHS Foundation Trust, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | | | - R Voegeli
- DSM Nutritional Products Ltd, Kaiseraugst, Switzerland
| | - R D Unwin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Core Technology facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT, UK
| | - M J Sherratt
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - R E B Watson
- Centre for Dermatology Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, and Salford Royal NHS Foundation Trust, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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7
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Sterling S, Mason KE, Anex DS, Parker GJ, Hart B, Prinz M. Combined
DNA
Typing and Protein Identification from Unfired Brass Cartridges,,,. J Forensic Sci 2019; 64:1475-1481. [DOI: 10.1111/1556-4029.14042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 12/25/2022]
Affiliation(s)
| | - Katelyn E. Mason
- Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Deon S. Anex
- Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | | | - Bradley Hart
- Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Mechthild Prinz
- John Jay College of Criminal Justice 524 W. 59th St. New York NY 10019
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8
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Hameury S, Borderie L, Monneuse JM, Skorski G, Pradines D. Prediction of skin anti-aging clinical benefits of an association of ingredients from marine and maritime origins: Ex vivo evaluation using a label-free quantitative proteomic and customized data processing approach. J Cosmet Dermatol 2019; 18:355-370. [PMID: 29797450 DOI: 10.1111/jocd.12528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2018] [Indexed: 01/18/2023]
Abstract
BACKGROUND The application of ingredients from marine and maritime origins is increasingly common in skin care products, driven by consumer expectations for natural ingredients. However, these ingredients are typically studied for a few isolated in vitro activities. OBJECTIVES The purpose of this study was to carry out a comprehensive evaluation of the activity on the skin of an association of ingredients from marine and maritime origins using label-free quantitative proteomic analysis, in order to predict the clinical benefits if used in a skin care product. METHODS An aqueous gel containing 6.1% of ingredients from marine and maritime origins (amino acid-enriched giant kelp extract, trace element-enriched seawater, dedifferentiated sea fennel cells) was topically applied on human skin explants. The skin explants' proteome was analyzed in a label-free manner by high-performance liquid nano-chromatography coupled with tandem mass spectrometry. A specific data processing pipeline (CORAVALID) providing an objective and comprehensive interpretation of the statistically relevant biological activities processed the results. RESULTS Compared to untreated skin explants, 64 proteins were significantly regulated by the gel treatment (q-value ≤ 0.05). Computer data processing revealed an activity of the ingredients on the epidermis and the dermis. These significantly regulated proteins are involved in gene expression, cell survival and metabolism, inflammatory processes, dermal extracellular matrix synthesis, melanogenesis and keratinocyte proliferation, migration, and differentiation. CONCLUSIONS These results suggest that the tested ingredients could help to preserve a healthy epidermis and dermis, and possibly to prevent the visible signs of skin aging.
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Affiliation(s)
- Sebastien Hameury
- Research & Development Department, Laboratoires B.L.C. Thalgo Cosmetic S.A., Roquebrune-sur-Argens, France
| | | | | | | | - Dominique Pradines
- Research & Development Department, Laboratoires B.L.C. Thalgo Cosmetic S.A., Roquebrune-sur-Argens, France
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9
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Cole LM, Clench MR, Francese S. Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:77-123. [PMID: 31236840 DOI: 10.1007/978-3-030-12298-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science.This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies.In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution.With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies.Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest.
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Affiliation(s)
- L M Cole
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - M R Clench
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - S Francese
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK.
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10
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Petushkova NA, Rusanov AL, Zgoda VG, Pyatnitskiy MA, Larina OV, Nakhod KV, Luzgina NG, Lisitsa AV. Proteome of the human HaCaT keratinocytes: Identification of the oxidative stress proteins after sodium dodecyl sulpfate exposur. Mol Biol 2017. [DOI: 10.1134/s0026893317050259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Höper T, Mussotter F, Haase A, Luch A, Tralau T. Application of proteomics in the elucidation of chemical-mediated allergic contact dermatitis. Toxicol Res (Camb) 2017; 6:595-610. [PMID: 30090528 PMCID: PMC6062186 DOI: 10.1039/c7tx00058h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/07/2017] [Indexed: 12/23/2022] Open
Abstract
Allergic contact dermatitis (ACD) is a widespread hypersensitivity reaction of the skin. The cellular mechanisms underlying its development are complex and involve close interaction of different cell types of the immune system. It is this very complexity which has long prevented straightforward replacement of the corresponding regulatory in vivo tests. Recent efforts have already resulted in the development of several in vitro testing alternatives that address key steps of ACD. Yet identification of suitable biomarkers is still a subject of intense research. Search strategies for the latter encompass transcriptomics, proteomics as well as metabolomics approaches. The scope of this review shall be the application and use of proteomics in the context of ACD. This includes highlighting relevant aspects of the molecular and cellular mechanisms underlying ACD, the exploitation of these mechanisms for testing and biomarkers (e.g., in the context of the OECD's adverse outcome pathway initiative) as well as an outlook on emerging proteome targets, for example during the allergen-induced activation of dendritic cells (DCs).
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Affiliation(s)
- Tessa Höper
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Franz Mussotter
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Andrea Haase
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Andreas Luch
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Tewes Tralau
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
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Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim DS, Shin DH, Bianucci R, Haynes PA. Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0373. [PMID: 27644972 PMCID: PMC5031639 DOI: 10.1098/rsta.2015.0373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 05/18/2023]
Abstract
We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jana Jones
- Department of Ancient History, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Prathiba Ravishankar
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Dylan Xavier
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Do Seon Lim
- Department of Dental Hygiene, College of Health Sciences, Eulji University, Sungnam, South Korea
| | - Dong Hoon Shin
- Department of Anatomy, Seoul National University, College of Medicine, Seoul, South Korea
| | - Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Legal Medicine Section, University of Turin, 10126 Turin, Italy UMR 7268, Laboratoire d'Anthropologie bio-culturelle, Droit, Étique and Santé (ADÉS), Faculté de Médecine de Marseille, 13344 Marseille, France
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Tan Q, Wang W, Yang C, Zhang J, Sun K, Luo HC, Mai LF, Lao Y, Yan L, Ren M. α-ketoglutarate is associated with delayed wound healing in diabetes. Clin Endocrinol (Oxf) 2016; 85:54-61. [PMID: 26921880 DOI: 10.1111/cen.13047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/06/2016] [Accepted: 02/21/2016] [Indexed: 01/13/2023]
Abstract
AIM A high level of matrix metalloproteinase 9 (MMP-9) is a predictor of poor wound healing in diabetic foot ulcers. In skin keratinocytes, site-specific DNA demethylation plays an important role in MMP-9 expression. Ten-eleven translocation enzyme 2 (TET2) protein, one member of TET family, could rely on α-ketoglutarate (α-KG) as cosubstrate to exhibit catalytic activity of DNA demethylation. Here, we aimed to explore the changes of α-KG and its relationship with MMP-9 and TET2 during diabetic wound healing. METHODS Seventy-one cases of patients with diabetic foot ulcers and 53 cases of nondiabetic ulcers were enrolled. Serum, urine and wound fluids were collected for measurement of α-KG levels and MMP-9 expression. Skin tissues were collected for the measurement of TET2 and MMP-9 expression. Clinical parameters were collected, and transcutaneous oxygen pressure (TcPO2) levels of feet were detected. RESULTS The levels of α-KG, TET2 and MMP-9 were significantly increased in diabetic wound compared with nondiabetic wound (P = 0·010, 0·016 and 0·025). There was a significant correlation between a low TcPO2 and a high α-KG level of wound fluids (r = -0·395, P = 0·002). Further analysis showed that α-KG concentration had a positive correlation with both haemoglobin A1c (HbA1C) and 2 h postprandial blood glucose (PBG) (r = 0·393, P = 0·005; r = 0·320, P = 0·025, respectively). CONCLUSIONS The levels of α-KG, TET2 and MMP-9 were significantly increased in diabetic wound compared with nondiabetic wound. Elevated α-KG was related to local hypoxia ischaemia status and systematic poor glycaemic control.
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Affiliation(s)
- Qin Tan
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Wei Wang
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Chuan Yang
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Jinglu Zhang
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Kan Sun
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Heng Cong Luo
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Li Fang Mai
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Yu Lao
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Li Yan
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Meng Ren
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
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14
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Kendall AC, Pilkington SM, Sassano G, Rhodes LE, Nicolaou A. N-Acyl ethanolamide and eicosanoid involvement in irritant dermatitis. Br J Dermatol 2016; 175:163-71. [PMID: 26947140 DOI: 10.1111/bjd.14521] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Sodium lauryl sulfate (SLS) and ultraviolet radiation (UVR) are two commonly encountered cutaneous inflammatory stimuli. Differing histopathological and clinical features implicate involvement of alternative inflammatory pathways; bioactive lipid mediators (eicosanoids, endocannabinoids and sphingolipids) are likely candidates for regulation of the divergent inflammatory responses. OBJECTIVES To assess comprehensively bioactive lipid involvement in SLS- and UVR-induced inflammatory responses, to provide a better understanding of bioactive lipid mediator pathways in irritant inflammation. METHODS Buttock skin from 10 healthy volunteers was treated with two minimal erythema doses of UVR (275-380 nm, peak 305 nm) or an SLS dose optimized for each individual, to produce a comparable, moderate erythema. Punch biopsies were taken 24 h postchallenge and from untreated skin, and separated into dermis and epidermis. Lipids [including 15 prostanoids, 15 hydroxy fatty acids (HFAs), nine endocannabinoids and related N-acyl ethanolamides (NAE), and 21 sphingolipids] were extracted and quantified using liquid chromatography-tandem mass spectrometry. RESULTS Increased epidermal NAE and HFA expression was observed in response to SLS but not UVR-induced low-level inflammation. Significant changes following SLS treatment included augmented levels of NAE, possessing proinflammatory and some reported anti-inflammatory properties, with 3·7-fold (P = 0·02) and threefold (P = 0·01) increased expression of palmitoyl and stearoyl ethanolamides, respectively, in addition to 1·9-fold (P = 0·02) increased expression of 12-hydroxyeicosatetraenoic acid. CONCLUSIONS The differential bioactive lipid upregulation implicates their involvement in skin irritant responses, potentially reflecting roles in inflammatory cell recruitment and subsequent resolution of inflammation, giving scope for new treatment approaches to irritant dermatitis.
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Affiliation(s)
- A C Kendall
- Manchester Pharmacy School, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, U.K
| | - S M Pilkington
- Dermatology Centre, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, U.K.,Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, U.K
| | - G Sassano
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, MK44 1LQ, U.K
| | - L E Rhodes
- Dermatology Centre, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, U.K.,Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, U.K
| | - A Nicolaou
- Manchester Pharmacy School, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, U.K
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Parkinson E, Boyd P, Aleksic M, Cubberley R, O'Connor D, Skipp P. Stable isotope labeling method for the investigation of protein haptenation by electrophilic skin sensitizers. Toxicol Sci 2014; 142:239-49. [PMID: 25145658 DOI: 10.1093/toxsci/kfu168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The risk of contact sensitization is a major consideration in the development of new formulations for personal care products. However, developing a mechanistic approach for non-animal risk assessment requires further understanding of haptenation of skin proteins by sensitizing chemicals, which is the molecular initiating event causative of skin sensitization. The non-stoichiometric nature of protein haptenation results in relatively low levels of modification, often of low abundant proteins, presenting a major challenge for their assignment in complex biological matrices such as skin. Instrumental advances over the last few years have led to a considerable increase in sensitivity of mass spectrometry (MS) techniques. We have combined these advancements with a novel dual-labeling/LC-MS(E) approach to provide an in-depth direct comparison of human serum albumin (HSA), 2,4-dinitro-1-chlorobenzene (DNCB), 5-chloro-2-methyl-4-isothiazolin-3-one (MCI), trans-cinnamaldehyde, and 6-methyl coumarin. These data have revealed novel insights into the differences in protein haptenation between sensitizers with different reaction mechanisms and sensitizing potency; the extreme sensitizers DNCB and MCI were shown to modify a greater number of nucleophilic sites than the moderate sensitizer cinnamaldehyde; and the weak/non-sensitizer 6-methyl coumarin was restricted to only a single nucleophilic residue within HSA. The evaluation of this dual labeling/LC-MS(E) approach using HSA as a model protein has also demonstrated that this strategy could be applied to studying global haptenation in complex mixtures of skin-related proteins by different chemicals.
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Affiliation(s)
- Erika Parkinson
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Pete Boyd
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Maja Aleksic
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, MK44 1LQ, UK
| | - Richard Cubberley
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, MK44 1LQ, UK
| | - David O'Connor
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, SIP Suzhou, Jiangsu Province 215123, China
| | - Paul Skipp
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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